T-BAS

T-BAS performs phylogenetic placement and analysis of DNA sequences to support fungal systematics, diversity, ecology, and functional biology using a reference phylogeny of Pezizomycotina (Ascomycota) constructed from six loci.

Key Features:

• Core reference phylogeny: A curated phylogenetic framework comprising 979 taxa (including 23 outgroup taxa) representing 61 orders, 175 families, and 496 genera of Pezizomycotina.
• Multi-locus framework: Reference phylogeny and alignments are based on six loci: nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, and RPB2.
• Curated alignments: Provision of highly curated single- and multi-locus alignments selectable by clade from the reference tree.
• Phylogenetic placement methods: Placement of user sequences using BLAST or phylogeny-based approaches.
• Support for diverse sequence types: Designed to handle large datasets from Sanger sequencing of fungal cultures and alignable short reads from environmental amplicons.
• Metadata visualization: Visualization of user-supplied metadata mapped directly onto the phylogenetic tree.

Scientific Applications:

• Fungal systematics: Delimiting and evaluating relationships among taxa within Pezizomycotina using multi-locus phylogenies.
• Diversity studies: Assessing taxonomic diversity and distribution of fungal lineages using sequence placement and reference alignments.
• Ecology: Interpreting environmental amplicon data by placing short reads into a curated phylogenetic context.
• Functional biology: Linking phylogenetic placement to ecological or functional traits through metadata mapping on the tree.

Methodology:

Reference phylogeny constructed from sequence alignments of six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2) for 979 taxa; curated single- and multi-locus alignments available for download; sequence placement performed using BLAST or phylogeny-based approaches.